Francesco Giorlando

Musings on Research, Tech and Medicine Dr Giorlando is a clinician-scientist with interests in neuroscience, psychophysics, addiction and temporal perception. He implements high-performance computing and electronic systems for research and enjoys hacking with digital media and sustainable technologies.

Francesco Giorlando

Musings on Research, Tech and Medicine Dr Giorlando is a clinician-scientist with interests in neuroscience, psychophysics, addiction and temporal perception. He implements high-performance computing and electronic systems for research and enjoys hacking with digital media and sustainable technologies.

this post was previously published on my old website, there’ll be a few of those older but useful posts that I’ll be migrating over in the next little while…
Molecules are beautiful things, intricate and infinitely variable. As part of research publications it can be useful to catch them from their best angles. This short post gives some tips on how to present molecules in publications.
Our model for today is Prostaglandin-F2&#945 There are a number of chemical databases and ways of expressing molecular identities.

Scientific computing increasingly involves handling large amounts of raw data. This is particularly the case for neuroimaging. With increases in processing speed outpacing storage speed, disk i/o has become a limiting factor in many computing applications, especially in multi-user systems.
For my consulting work with GreenAnt Networks, I was asked to build a high-speed disk array for scientific computing and virtual machine storage. This is a brief build log and performance test of the outcome.

Introduction Scientific publishing is undergoing a transition from corporate-controlled, for-profit publishing to more open models. While “Open-Access”, is part of this, there are a number of considerations important in true “Open Publishing”:
Free access to the public (who pays for most of the research via their taxes!) Free submission of articles by authors Open Data - where original data and analysis workflows are made public Creative Commons - otherwise known as Copyleft, where rights are retained by the author but the content is usable with attribution Transparency of the review process (with or without anonymity) Open software, standards and tools used in the publication process This post will focus on item (6) from above.

Sharing MRI data with colleagues can be a time-consuming exercise. The files are often large and data-sets need to be viewable in a flexible fashion. Rich features assist the communication of results, including:
3D viewing flexible slicing overlay of specific volumes While there are many software packages for running on the desktop, there’s nothing better than being able to point to a simple HTML link and open the scan data in a prepared format.

LaTeX is a fantastic way to create and display print-ready scientific documents. There are a number of different ways to edit and produce LaTeX documents, which we’ll revist in a future post. In this post, I want to deal with one of the major issues that people find difficult with LaTeX: tables.
LaTeX can certainly produce any type of table you’d like to create, but it does so in a way that can be very difficult to follow visually.

In the process of building a new personal website, I hunted around for static website engines. My previous website used an engine called habari, but development of the Habari Project is discontinued and I was interested in writing posts in markdown instead of plain HTML.
So let’s get a few questions answered immediately:
Why a static engine? What is markdown? A static website engine converts an intermediate syntax into HTML.

If you’ve ever noticed the 3D images of brain structures on Wikipedia, you may have been curious where they are sourced from.
It turns out that they are generated from a freely accessible Japanese database, the Life Sciences Database Archive. This database is licensed under Creative Commons.
It includes anatomical models that can be downloaded as well as other public databases including gene expression databases. The anatomical models can be downloaded and browsed online at the Body Parts 3D site.

I recently attended a great symposium for time researchers in Tokyo. It was a fantastic to have a chance to exchange thoughts about new theories of psychological time and to see some very elegant experiments. The conference website is here: Time in Tokyo Symposium.
For the Symposium, I prepared a theoretical discussion of the specious present, considering how we may explore neurophenomenology with reference to recent neuroscientic findings. The slides for the talk are available here:

NDVI is an acronym for Normalised Difference Vegetation Index. It’s a very interesting measure of plant photosynthesis and health derived from measuring the difference in near-infrared and visual reflectance. I’ve recently been exploring its use for plant monitoring; here are a few calibration images.
[NDVI=\frac{NIR-VIS}{NIR+VIS}]
The original image is on the left, with NDVI on the right
These images were shot using a full-spectrum modified Sony A7 camera with OM Zuiko 21mm/3.